Halo 3: The Ark of the Covenant
by Sammy the Spartan
Summary: The Covenant has been broken. The Elites, betrayed by the Prophets, have sworn revenge. The Prophets will stop at nothing to begin the Great Journey. Earth is under attack. Only Master Chief and his allies can save it.
1. Prologue

_Author's Note-This prologue is the end of Halo 2, the fight with Tartarus rewritten to better work with this story. All dialogue from the ending cutscene is verbatim._

_Any of the characters, technology and such appearing in Halo, Halo 2 or any of the novels are property of Bungie and Microsoft._

**Delta Halo, Control Room**

The Arbiter backed off as Tartarus came charging at him. He ducked a swing from the Brute's hammer, and then thrust with his two-pronged plasma sword. It bounced harmlessly off of Tartarus' overshield, as the Brute smiled wickedly. He slammed the Arbiter with his body, and the Elite fell to the ground. He raised the hammer, preparing to deal the death blow.

"Now you pay the price of your treachery, Arbiter." the Brute growled. He started to bring the hammer down, but the Elite was quicker. He rolled out of the way, feeling the vibration of the hammer's impact on the ground. He leaped to his feet, and the Brute spun to face him. The Arbiter looked around the platform, seeing the broken bodies of his brothers. He looked back at the Brute with a look colder than the vacuum of space.

"No Tartarus. Now you pay the price of yours." A shot from Sergeant Johnson's Particle Beam rifle pierced the Brute's overshield, and the Arbiter dashed forward. For a brief moment, a flicker of fear flashed across the Brute's face. That look was replaced by the glazed expression of death, as the Arbiter pulled his sword out of the ape's chest, and the body collapsed to the ground.

"Now, ma'am!" Sergeant Johnson shouted. Commander Miranda Keyes leaped from the focusing platform she had been waiting on for Johnson's mark. She rolled as she landed on another platform on the lower tier moving in the opposite direction. She ducked as a platform on the upper tier passed right over her, missing by mere centimeters. She dropped onto the main fire control platform, and snatched the Index crystal right out of the air it was hovering in.

The platform rumbled as a cancellation pulse discharged from the generator powering up Halo's main weapon. It screamed into the vacuum of space, towards the center of the ring where the raging firestorm, the massive amount of destructive energy that could exterminate a large portion of the sentient life in the galaxy, was preparing to fulfill its deadly purpose. The pulse hit the center of the energy mass, and with a large explosion that filled the vacuum surrounding the ring, the energy dissipated, and Halo was once again silent.

On the fire control platform, a hologram appeared in front of Keyes. Two half-spheres were slightly apart, but she couldn't decipher the tangle of images sandwiched between them. She turned to look, as the Sergeant came floating down, hanging off of 343 Guilty Spark.

Commander Keyes addressed the glowing Monitor. "What's that?"

"A beacon." The Monitor seemed to stare at the pair of humans with it's light bulb-like eye, as if they should know what was happening.

"What's it doing?" she urged the increasingly obnoxious AI.

"Communicating at superluminal speed, with a frequency of…" Keyes cut the construct off.

"Communicating with what?" she persisted.

"The other installations."

"Show me."

The image began to resolve. The tangle separated into individual Halo installations. "Fail-safe protocol- In the event of unexpected shutdown, the entire system will move to standby status. All remaining platforms are ready for remote activation."

"Remote activation? From here?" Keyes asked, an edge of worry in her voice.

"Don't be ridiculous," the Monitor retorted.

Sarge stepped forward, pointing at the construct."Listen Tinkerbell, don't make me…"

Keyes stopped him with a hand on his shoulder. She was feeling the Sergeant's impatience, too, but there were more important things to worry about. "Then where? Where would someone go to activate the other rings?"

"Why, the Ark," the Monitor replied. "Of course."

The two humans started as they heard Arbiter come up behind them. "And where Oracle, is that?" the Elite asked reverently.

**Earth Orbit, Forerunner Ship**

Master Chief felt the Forerunner ship rumble as it decelerated abruptly out of slipspace and emerge into normal space. He ran a status check on his MJOLLNIR Mark VI armor, finding everything was operating optimally. He ran his suit's limited sensors, hoping to discern his location, and when he picked up radio signals, he knew where he had arrived.

Earth. The Covenant invasion had begun.

"We've got a new contact," a garbled transmission came. "Unknown classification."

"It isn't one of ours," Admiral Hood said. "Take it out."

"This is Spartan 117," the Master Chief broke in. "Can anybody hear me?"

"Isolate that signal," the Admiral ordered. "Master Chief, mind telling me what you're doing here?"

The Spartan straightened up. "Sir. Finishing this fight."

**Covenant Holy City of High Charity, Mausoleum of the Arbiter**

The Covenant holy city of High Charity was silent, as debris from the Flood bodies floated about. Tentacles snaked through the gaps in the malfunctioning door. "Silence fills the empty grave," the evil voice of the Flood Gravemind echoed through the quiet Mausoleum. "Now that I have come. But my mind is not at rest, for questions linger. I will ask, and you will answer." A tentacle reached for the small figure on the holographic display.

Cortana reached out a holographic hand to stop the appendage, not that it would do any real good, but the tentacle stopped anyway. "All right," she said warily. "Shoot."


	2. Redemption

**Control Room, Delta Halo**

Johnson, Keyes and the Arbiter all waited for 343 Guilty Spark to answer.

With a mechanical sigh, the floating construct said, "That information is not available. The Forerunners left only minimal reference to the Ark in Halo's data banks," he said, perturbed at their lack of knowledge. "If I have inferred their reason for doing so correctly, they did not want the Flood to find its location. I do believe it was an emergency base, in the case that the Installation network was activated."

"Damn," Sergeant Johnson grunted. "Where the hell does that leave us?"

"I believe I may hold the answer," the Arbiter said gravely.

"Any information you may have is important. Stopping Truth from activating the Halo network is all that matters," Keyes said quietly.

The Arbiter nodded in agreement. "The coordinates for your planet were discovered on a holy relic of the Forerunners. The Council of the Hierarchs meditated on this discovery and concluded that the coordinates would yield something of great importance. The Prophet of Regret arrogantly took it upon himself to investigate, and paid the price for it."

There was a pause as it sank in to Commander Keyes' mind. "Is that all you can tell me?" she asked.

"It is."

"Then we have no time to waste. Truth has likely ordered a full invasion of Earth, and is ready to kill every single human to get the Ark. We have to warn them."

The Elite nodded. "And I must inform my brothers in the fleet of the Prophets' treachery."

"Ma'am, it's a damn long shot," Johnson said unhappily.

"I'm aware of what it is, Sergeant, but our options are limited." She looked at the Marine. "It's all we have."

"How're we gonna get off this ring? The damn Flood took our ship," Johnson growled.

"You will come with us," a deep voice said from above. The humans and the Elite looked up to see the half-jawed Elite Commander, Rtas Vadumee, standing on the platform that led out of the Control Room. "The fleet is back in our hands. The traitorous Brutes and Jackals have all been eliminated." He leaped down to join them. "We can no longer afford to be enemies."

"That's fine and dandy, but how're we gonna explain this to everybody, human and Elite, fighting on Earth?" Johnson asked angrily. "Neither side's gonna stop shooting just because a few of us are pals now. It's gonna take a lot more than an explanation to end this war."

"And that is why we will use the Oracle," said the Arbiter. "Our brothers will believe his holy testimony."

"And I can contact Fleet HQ, send one of my command codes, and give a short explanation. That code will tell them that I'm not under any duress," Keyes said. "But it will take time to stop the fighting, with all the tension and the years of conflict between our peoples, no matter how high the orders come from. And time is something we don't have. Stopping Truth comes first. If he activates the Ark…" she trailed off.

"Alright, so first order of business: Get the hell back to Earth and stop that son of a bitch," said Johnson.

"That seems to be the best course of action," Vadumee said in agreement.

"But ain't we forgetting somebody?" Johnson said. "What about the Chief?"

"The last radio contact we had with him was shortly before the High Charity fleet jumped in," said Keyes. "The island the Chief was on was destroyed from orbit. The interference of all that energy disrupted his signal, and when we could finally punch through, we couldn't pick it up."

"Well he's gotten outta tighter situations before," said Johnson. "If anybody could have survived, he would have."

"You speak of the Demon?" said the Arbiter. "No, he is not dead. He and I met in the depths of this ring. When the traitor, Tartarus, knocked me into the pit, I fell into the darkness. But I did not die. Some kind of Flood intelligence captured me, and when I awoke, the Demon was there as well," the Arbiter related. "The parasite sent us to search for the Index and stop the Hierarchs from activating the ring."

Johnson and Keyes were both relieved and rattled at the same time. A Flood intelligence?

Keyes came out of it first "Where is he?"

"We were each there grasped in tentacles of the parasite, being told we had to stop the ring from activating, then the Demon disappeared. There was a flash, and I was suddenly outside of the control room."

"Aha!" Every being turned, and Guilty Spark was hovering there looking back at them, who until now had been obliviously hovering in the air. "That explains the unauthorized use of this installation's transport network. But a Flood intelligence that has the sentience to try and prevent the activation of the installation? This is simply unacceptable. This cannot be allowed. Reclaimer, you must insert the Index!"

"Where was the Master Chief transported to?" Keyes asked, completely ignoring its instructions.

"To the meddler's installation, but that is irrelevant, this installation must be..." It quickly stopped talking as Johnson cocked his gun threateningly.

"The Oracle must be speaking of High Charity," the Arbiter said.

"Contact was lost with High Charity during our brothers' revenge on the traitors," Commander Vadumee said. "The Flood seem to have commandeered the human ship to invade the city. According to our ship's sensors, the Ancestor's ship that powered the city has disengaged, and is no longer in this system."

"Probably Truth escaping," said Keyes.

"And if I know the Chief, he managed to get on board too," Johnson said with a smile.

"If the Demon sets his mind to stopping that traitor, he will," said the Arbiter, who knew from experience what tenacity the Spartan had.

"It is in his hands," said Keyes gravely. "Now we have to stop the war."

"What about the Flood up on your city?" Johnson said. "It can use slipspace, and I'm betting the Flood can figure out how to make that happen."

"The Ancestors' ship powered High Charity," said the Arbiter. "Its engines were used to propel the city through slipspace. Without an equivalent power source, the Flood are stranded here."

"It makes me damn nervous to leave that thing sitting there, full of those disgusting mothers," Johnson replied obstinately.

"The parasite is resilient," Vadumee agreed. "What is your decision, Supreme Commander?"

It was suddenly silent, until the Arbiter started, realizing he was being addressed by his former rank. A low growl emerged from his throat, and baring his four jaws, he said quietly "What did you call me?"

"The Prophets took your life from you," Vadumee said with a smile. "You were made the Arbiter by their decision. But you earned your rank, and our allegiance, long ago. We are no longer deceived by their treachery. We will follow you." The humans shifted uncomfortably, knowing that the rank was earned by killing humans in the war. "Salute!" Vadumee yelled out.

"Hail!" was heard echoing throughout the large chamber. The four beings looked up to see the surviving Elites from Vadumee's combat group at attention on the platform above the control room. Silence reigned.

The former Arbiter looked long at his brothers, feeling once again the respect and loyalty that he once commanded. He knew that no longer was he just a discarded tool. His heresy, so called by the Prophets, was nothing but a lie. He was himself again. A warrior, with honor.

"Very well," he said. "We are leaving the ring. Get your men on the Phantoms, and to the nearest ship," he ordered.

"Move out!" Vadumee ordered his Sangheili. They left the control room, leaving the two humans and Elites alone. He turned back to the Supreme Commander. "What is your command for the fleet?"

"We will concentrate all firepower on High Charity, until it has been blown to dust!" he snarled. "We cannot afford to leave the parasite alive."

"Now that is my kind of plan," Johnson said happily.

"When it is no more, we will proceed to Earth, and stop the crusade against your world." Turning to Guilty Spark, he said, "Oracle, you must come with us."

"Foolish meddlers! That is unacceptable. You must activate this installation!" the Monitor protested.

"We need your help to activate the Ark," Keyes lied, knowing the Elites needed the construct to stop the Covenant fleet.

"Oh, really!" he said happily. "Splendid. What are we waiting for? There is no time to waste and much to do!" At his command, the floating platforms in the control room were rearranged into a set of stairs leading out of the control room. "Come, we must hurry! I will safeguard the Index." He called the small object from Keyes' hand and locked it within himself, and then happily zipped up to the upper platform and hovered there, silently waiting for the four beings.

"Go, take one of the Phantoms to the ship," the Supreme Commander said to Vadumee. "There is something I must do. Alone. I will board the second Phantom when I am ready."

"Yes Supreme Commander."

"They are in your care," the Supreme Commander said, gesturing at the humans. "Await me on the command deck."

"It is as you command," said Vadumee. Turning to Keyes and Johnson he said, "Come. Let our alliance begin with the breaking of the Covenant."

"That's what I like to hear, cowboy," Johnson said. "Let's roll."

The group began climbing the platform steps, Guilty Spark zipping ahead of them.

"Do anymore of your kind survive?" Vadumee asked.

"Just us two and a few Marines back where I took the Scarab," Johnson said. "They're waiting there for dust off."

"Everyone else was either killed, or taken by the Flood," Keyes said sadly.

"That is unfortunate," Vadumee said gravely. "We will pick up your warriors, and then join the fleet. Soon, the traitors will be in our grasp. They will pay for the lives they have cost. Both Sangheili, and human." His jaw and a half gnashed in anger as they walked out of the control room.

The former Arbiter turned back as soon as Vadumee and the humans had left him alone, and walked to the edge of the platform. He pulled off his helmet, the helmet of the Arbiter. Before, he had felt honored to wear the armor, used to uphold the Covenant throughout its long history. Now, knowing the truth, it represented his enslavement by the Hierarchs. That's all every Arbiter had ever been. All any Elite had ever been. Slaves, to a lie.

No more, he thought. With an angry bellow, he hurled the helmet into the pit below him. Removing each component, he also threw them into the abyss. When he was finished, he turned and walked up the steps, leaving the control room, and his enslavement behind him. Never again.

**Earth Air-Space, Forerunner Ship**

"I don't have time to get a full report, son," the Admiral said over the radio, explosions echoing in the background, "But I need to know what happened. Where is Commander Keyes?"

"Sir, we found another Halo installation. We encountered the Covenant, and the Flood. I was separated from the UNSC forces when I went after Truth to retrieve the Index, and stop the activation of Halo," the Spartan said. "I am in the process of completing that mission."

There was a slight pause, then the Admiral continued, "Proceed Master Chief." There was another pause, as the Admiral watched the Forerunner ship on the _Cairo_'s radar. "Be advised that the ship you're on is not engaging any UNSC forces. It appears to be heading for the surface." Another explosion could be heard over the channel. "Truth wants something down there. It's your job to make sure he doesn't get it."

"Understood, sir."

"In the meantime, I'm sending some Longswords to try and slow that ship down. Good luck Spartan." He closed the channel, and then smiled to himself. If anyone can stop the Covenant from getting what they want, it's that Spartan.

Master Chief looked around open vacuum cylindrical segment he had hitched his ride in, looking for a way into the interior of the ship. He spotted what looked like a maintenance hatch, and went towards it. Without Cortana, he wouldn't know what was on the other side, but what he did know is that it wouldn't be friendly. He smiled to himself. No one ever was happy to see him. He unholstered his SMGs, as he examined the panel next to the hatch, and hit the opening mechanism. The hatch slid silently into the wall. Monitoring his motion sensors, he checked for an enemy's presence, but it detected nothing. He peered into the hatch, keeping his body out of the doorway in case of enemy fire. Red emergency lighting stretched up the hatch. He couldn't see any Covenant, but to check for camoflauged enemies, he activated his suit's thermal scanners. No heat signatures were registered. Satisfied, he crouched down, and advanced into the hatch, weapons at the ready.


End file.
